Although cross-functional conflicts occur among departments, empirical research on the inherent mechanism remains scant. As conflict appears to be an element in innovation, by using a symbiotic approach combining traditional Confucian values and mainstream Western theories, this study of 135 Chinese high-tech companies investigates how various cross-functional conflict types influence cross-functional effectiveness, which in turn influences innovation performance. Results show an inverted U-shaped relationship for cross-functional task conflict and a negative relationship for cross-functional relationships on cross-functional effectiveness and innovation performance. Cross-functional effectiveness has a complementary mediation effect on the relationship between cross-functional task conflicts and innovation performance, and an indirect mediation effect on the relationship between cross-functional relationship conflicts and innovation performance. Trust moderates the relationship between cross-functional task conflict and cross-functional effectiveness, demonstrating a U-shaped relationship. Results are inconclusive about trust’s moderating effect between relationship conflict and cross-functional effectiveness. This study offers executives new guidelines for managing conflict and trust to improve their high-tech firm’s innovation climate.